The mutation frequencies are sampled according to Wright's formula (see Methods), and hence mutations are very rare for some variants. Using 1000 affected and 1000 unaffected individuals, mutations are on average observed at only 49.4% of the variants (sd: 4.9%). This means that when e.g. 100 variants are sampled, on average 49.4 variants contain at least one mutation, and are hence tested for association. This level is in concordance with the level from human resequencing studies [5],[7],[16].
